Re: [AMBER] Amber18 compilation error on a Linux CPU cluster

From: Bill Ross <>
Date: Sun, 23 Dec 2018 11:17:50 -0800

Search on enable-mpi? I saw one possibly useful 2017 response/suggestion from dac on this.

<div>-------- Original message --------</div><div>From: Sundar <> </div><div>Date:12/23/2018 10:40 AM (GMT-08:00) </div><div>To: David Case <>, AMBER Mailing List <> </div><div>Subject: Re: [AMBER] Amber18 compilation error on a Linux CPU cluster </div><div>
</div>I rerun everything from the tar files.

Serial installation was successful but mpi compilation fails with following
errors> ./configure -mpi gnu
Checking for updates...
Checking for available patches online. This may take a few seconds...

Available AmberTools 18 patches:

No patches available

Available Amber 18 patches:

No patches available


Using the AmberTools miniconda installation in
version 2.7.13

Obtaining the gnu compiler suite versions, e.g.:
     gcc -v
The C version is 4.9.2
The Fortran version is 4.9.2

Testing the gcc compiler:
     gcc -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o testp testp.c

Testing the g++ compiler:
     g++ -fPIC -o testp testp.cpp

Testing the gfortran compiler:
     gfortran -fPIC -O0 -o testp testp.f

Testing mixed C/Fortran compilation:
     gcc -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -c -o testp.c.o
     gfortran -fPIC -O0 -c -o testp.f.o testp.f
testp.c.o testp.f.o -lgfortran -w

Testing pointer size:
test_pointer_size test_pointer_size.c
Detected 64 bit operating system.

Testing flex: OK

Checking NetCDF...
    Using bundled NetCDF library.
    Using existing NetCDF in '/u/sundar/tools/amber18/amber18'

Checking for zlib: OK

Checking for libbz2: OK

Testing the g++ compiler with boost:
     g++ -fPIC testp.cpp -lboost_thread -lboost_system -o testp

Warning: Could not link to boost. Ensure boost-thread, boost-system and
boost headers are installed.
Warning: Failed command:
     g++ -fPIC -lboost_thread -lboost_system -o testp testp.cpp
Warning: Check boost.compile.err for error details.
Warning: Memembed functionality in packmol_memgen not available.

Configuring fftw-3.3 (may be time-consuming)...

Error: FFTW configure returned 1
       FFTW configure failed! Check the fftw3_config.log file
       in the /u/sundar/tools/amber18/amber18/AmberTools/src directory.
Configure failed due to the errors above!

$ tail $AMBERHOME/AmberTools/src/fftw3_config.log

checking for mpicc... no
checking for hcc... no
checking for mpcc... no
checking for mpcc_r... no
checking for mpxlc... no
checking for cmpicc... no
checking for MPI_Init... no
checking for MPI_Init in -lmpi... no
checking for MPI_Init in -lmpich... no
configure: error: could not find mpi library for --enable-mpi


On Sun, Dec 23, 2018 at 7:37 AM David Case <> wrote:

> On Sat, Dec 22, 2018, Sundar wrote:
> >I did the serial installation first and then did "./configure -mpi gnu".
> >That's when I got this error message.
> What I don't understand is why you were not prompted to apply the
> updates when you did the original serial installation.
> >
> >Would you recommend a fresh serial installation from the tar files and try
> >the parallel version?
> Yes....good luck....dac

Sundar Thangapandian
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Received on Sun Dec 23 2018 - 11:30:02 PST
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